F.A.R.O.G. FORUM, Vol. 5 No. 8

https://digitalcommons.library.umaine.edu/francoamericain_forum/1064/thumbnail.jp

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

Chiral, non-racemic, distally-bridged resorcin[4]arenes as models for use in asymmetric processes

The synthesis of enantiomerically pure, distally-bridged resorcinarenes 3 with various R groups (CH3, C5H11, C-11 H-23) is reported. The key step makes use of the Mannich reaction for attachment of a chiral diamine-line 2 across the cavity. Yields for this step are good to excellent. One of the bridged compounds exhibits modest activity (27% ee) as an enantioselective catalyst in the addition of diethylzinc to benzaldehyde

Retro-Mannich reactions of 3-alkyl-3,4-dihydro-2H-1,3-benz e oxazines and the synthesis of axially chiral resorcinarenes

Intermediates involved in the conversion of 3-alkyl-3,4-dihydro-2H-1,3-benz[e]oxazines into 2-N,N-dialkylaminomethylphenol derivatives, using morpholine and other high boiling secondary amines, have been identified and characterised. Additional experiments have established the involvement of o-quinone methide intermediates in the retro-Mannich reactions. Axially chiral resorcinarenes have been prepared by utilising the exchange reactions. (C) 2003 Elsevier Science Ltd. All rights reserved

The reductive cleavage of cyclic aminol ethers to N,N-dialkylaminoderivatives: Modifications to the Eschweiler-Clarke procedure

The reductive cleavage of cyclic aminol ethers to give N-alkylamino- derivatives in very high yields can be achieved using chlorotrimethylsilane in the presence of sodium cyanoborohydride: in the case of cyclic aminol ethers derived from formaldehyde the Eschweiler-Clarke reaction can be carried out in formic acid heated under reflux in the absence of formaldehyde

Use of bis-(aminol) ethers derived from N-(S)-(-)alpha-methylbenzylamine in reactions with resorcinarenes and double Mannich reactions

The synthesis of some chiral bis-(aminol)ethers are described. Reaction of a solution of the resorcin[4]arene derived from propanal with N,N-bis(methoxymethyl)-N-(S)-(-)-alpha-methylbenzylamine in toluene at 85 degrees C initially afforded a 1: 1 mixture of two diastereoisomeric tetrakis(benzoxazines). Further, heating of this mixture under reflux in ethanol for 24 h afforded the crystalline (alpha S),(S)-diastereoisomer in 77% yield. N,N-bis(ethoxymethyl)-N-(S)-(-)-alpha-methylbenzylamine and N,N-bis(ethoxymethyl)-N-(R)-(+)-alpha-methylbenzylamine were reacted with beta keto esters to afford a 1: 1 mixture of the diastereoisomeric double Mannich adducts. Two of the double Mannich adducts were converted into tricyclic ABE analogues of the alkaloid methyllycaconitine 1. (c) 2005 Elsevier Ltd. All rights reserved

An evaluation of genetic causes and environmental risks for bilateral optic atrophy.

PurposeTo assess the clinical utility of next-generation sequencing (NGS) for the diagnosis of patients with optic atrophy (OA).DesignRetrospective cohort study.Methods97 patients were referred to the McMaster University Medical Center (Hamilton, Ontario) for evaluation of bilateral OA. All patients were sent for NGS including a 22 nuclear gene panel and/or complete mitochondrial DNA (mtDNA) sequencing. Positive genetic test results and abnormal vibration sensation were compared in patients +/- environmental exposures or a family history.Results19/94 (20.2%) had a positive nuclear variant, of which 15/19 (78.9%) were in the OPA1 gene. No positive mtDNA variants were identified. The detection of a positive genetic variant was significantly different in patients who reported excessive ethanol use, but not in patients who smoke (0/19 (0%) vs. 19/78 (24.4%), P = 0.0164 and 4/22 (18.2%) vs. 15/74 (20.3%), P = 0.829, respectively). Patients with a positive family history were more likely to have a positive genetic variant compared to patients with a negative family history (P = 0.0112). There were significantly more excessive drinkers with an abnormal vibration sensation (P = 0.026), and with a similar trend in smokers (P = 0.074).ConclusionsAll positive genetic variants were identified in nuclear genes. We identified a potential independent pathophysiological link between a history of excessive ethanol consumption and bilateral OA. Further investigations should evaluate and identify potential environmental risk factors for OA